Hi Guys,
I've run into this error when trying to run some of Jenny's doctests. When
I look in the code of sqlgraph.py", line 269 seems to be at the wrong
indentation level. I get a new set of errors when I indent that line, so
I'm not sure if this is part of my problem or not... Comments?
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File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py", line 274,
in ensembl.adaptor.ExonAdaptor
Failed example:
slice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1',
end=100000, strand = -1)
Exception raised:
Traceback (most recent call last):
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/doctest.py",
line 1212, in __run
compileflags, 1) in test.globs
File "<doctest ensembl.adaptor.ExonAdaptor[5]>", line 1, in <module>
slice = coreDBAdaptor.fetch_slice_by_region('chromosome', '1',
end=100000, strand = -1)
File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py", line
688, in fetch_slice_by_region
sr = self._get_seqregion()
File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py", line
584, in _get_seqregion
seqRegion = self._create_seqregion()
File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py", line
565, in _create_seqregion
dnaAdaptor = self.get_adaptor('dna')
File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py", line
460, in get_adaptor
tbAdaptor = adaptorClass(name, itemClass=rowClass,
serverInfo=self.conn)
File "/Users/Robby/pyensembl-0.1.0/build/lib/ensembl/adaptor.py", line
214, in __init__
sqlgraph.SQLTable.__init__(self, name,
itemSliceClass=seqdb.SeqDBSlice, attrAlias=dict(seq='sequence'), **kwargs)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/sqlgraph.py",
line 269, in __init__
self.objclass(itemClass) # NEED TO SUBCLASS OUR ITEM CLASS
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/sqlgraph.py",
line 352, in objclass
subclassArgs=dict(db=self)) # bind itemClass
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/pygr-0.7-py2.5-macosx-10.3-fat.egg/pygr/classutil.py",
line 217, in get_bound_subclass
subclass_init(**subclassArgs)
TypeError: unbound method _init_subclass() must be called with
shadowClass instance as first argument (got nothing instead)
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